Research workbench
Crystal structure of ubix, an aromatic acid decarboxylase from the colwellia psychrerythraea 34H
Analyse Crystal structure of ubix, an aromatic acid decarboxylase from the colwellia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RHE
- Type
- protein
- Length
- 1,212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
- EC
- 4.1.1.-
- UniProt
- Q489U8
- Ligands
- FMN, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 202 | 43% helix, 15% strand | Q489U8 |
| B | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 203 | 43% helix, 15% strand | Q489U8 |
| C | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 201 | 42% helix, 15% strand | Q489U8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, D, E, B, C, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.82 | 0.83 | 123 | FMN, SO4 |
| 2 | 293 | 0.74 | 0.87 | 44 | FMN |
| 3 | 798 | 0.72 | 0.78 | 96 | empty |
| 4 | 275 | 0.55 | 0.76 | 24 | empty |
| 5 | 90 | 0.41 | 0.78 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1605 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1551 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 684 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 663 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 646 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RHE · Crystal structure of UbiX, an aromatic acid decarboxylase from the Colwellia… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q489U8
- Elsewhere: RCSB PDB 4RHE · PDBe 4RHE · UniProt Q489U8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.